Maize core-promoter atlas for synthetic biology applications
Auburn University presents a comprehensive activity atlas for 2,300 maize promoters, utilizing AI and barcoded STARR-seq assays to explore natural variations and design synthetic promoters. This tool enhances gene expression control in maize through validated design rules.
Overview
Auburn University's innovative research delves into the development of a high-confidence activity atlas for approximately 2,300 B73 maize promoters. This project employs a barcoded STARR-seq assay, coupled with advanced AI modeling, to investigate natural variations and propose synthetic promoters. The goal is to enhance the precision of gene expression control in maize, leveraging natural sequence variations and synthetic design to optimize promoter activity. This atlas serves as a crucial resource for researchers aiming to improve crop yields and resilience through genetic engineering.
Technical specifications
The research involves cloning reference and alternate haplotypes of maize promoters upstream of a fixed-UTR reporter. These are tested in maize protoplasts and validated for portability using Nicotiana. Activity is quantified using log2(RNA/DNA) ratios, considering core motifs, local GC content, and TF-binding contexts. An AI pipeline integrates iCREPCP and DeepSEED for SNP impact analysis and synthetic design. The project aims to release an open atlas, provide design rules, and validate a set of synthetic promoters, enhancing gene expression control.
Technology readiness level
Currently at TRL 3, this research has been validated through initial assays and AI modeling. Future validation steps are meticulously planned, including building barcoded reporter libraries, optimizing transformation protocols, and conducting comprehensive screens. The project is on track to refine its outputs and release a robust set of synthetic promoters by the end of the validation timeline.
About Auburn University
Auburn University is a comprehensive public land‑grant research university serving industry from its main campus in Auburn, Alabama. Companies engage through a research and technology park offering on‑site convening space and services, and via a Huntsville Research and Innovation Campus embedded in Cummings Research Park near Redstone Arsenal. A long‑standing cooperative education program and a statewide extension network link employers to student talent and field deployment across Alabama. Research is supported by competitive federal funding from agencies such as NSF, USDA, DoD, and NASA. The university’s Intellectual Property Exchange provides IP management, licensing, and commercialization support.
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